FAIRMol

Z56175908

Pose ID 3068 Compound 2210 Pose 358

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T05
L. major PTR1 L. major
Ligand Z56175908
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
42.7 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.55, H-bond role recall 0.33
Burial
88%
Hydrophobic fit
83%
Reason: strain 42.7 kcal/mol
strain ΔE 42.7 kcal/mol 2 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.986 kcal/mol/HA) ✓ Good fit quality (FQ -9.08) ✓ Good H-bonds (5 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (42.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-25.625
kcal/mol
LE
-0.986
kcal/mol/HA
Fit Quality
-9.08
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
5.09
cLogP
Strain ΔE
42.7 kcal/mol
SASA buried
88%
Lipo contact
83% BSA apolar/total
SASA unbound
580 Ų
Apolar buried
425 Ų

Interaction summary

HB 5 HY 24 PI 4 CLASH 5

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.827Score-25.625
Inter norm-1.149Intra norm0.164
Top1000noExcludedno
Contacts14H-bonds5
Artifact reasongeometry warning; 16 clashes; 1 protein clash; 3 cofactor-context clashes; high strain Δ 42.7
Residues
ARG17 ASP181 LEU188 LEU226 LEU229 MET183 MET233 NDP302 PHE113 SER112 SER227 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.55RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
356 1.922282705581446 -1.31548 -33.7258 4 19 0 0.00 0.00 - no Open
377 2.636046445329318 -1.08029 -27.1091 9 14 0 0.00 0.00 - no Open
358 2.827211891156502 -1.14937 -25.6248 5 14 11 0.65 0.33 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -25.625kcal/mol
Ligand efficiency (LE) -0.9856kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.080
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 365.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.09
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 50.57kcal/mol
Minimised FF energy 7.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 580.0Ų
Total solvent-accessible surface area of free ligand
BSA total 510.2Ų
Buried surface area upon binding
BSA apolar 425.5Ų
Hydrophobic contacts buried
BSA polar 84.7Ų
Polar contacts buried
Fraction buried 88.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1634.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1040.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)